Performs spatial tests on spatial cytometry data.

Usage

spicy(
  cells,
  condition,
  subject = NULL,
  covariates = NULL,
  from = NULL,
  to = NULL,
  imageIDCol = "imageID",
  cellTypeCol = "cellType",
  spatialCoordCols = c("x", "y"),
  alternateResult = NULL,
  verbose = FALSE,
  weights = TRUE,
  weightsByPair = FALSE,
  weightFactor = 1,
  window = "convex",
  window.length = NULL,
  BPPARAM = BiocParallel::SerialParam(),
  sigma = NULL,
  Rs = NULL,
  minLambda = 0.05,
  edgeCorrect = TRUE,
  includeZeroCells = FALSE,
  ...
)

Arguments

cells: A SummarizedExperiment or data frame that contains at least the variables x and y, giving the location coordinates of each cell, and cellType.
condition: A character specifying which column which contains the condition or `Surv` objects
subject: Vector of subject IDs corresponding to each image if cells is a data frame.
covariates: Vector of covariate names that should be included in the mixed effects model as fixed effects.
from: vector of cell types which you would like to compare to the to vector
to: vector of cell types which you would like to compare to the from vector
imageIDCol: The image ID if using SingleCellExperiment.
cellTypeCol: The cell type if using SingleCellExperiment.
spatialCoordCols: The spatial coordinates if using a SingleCellExperiment.
alternateResult: An pairwise association statistic between each combination of celltypes in each image.
verbose: logical indicating whether to output messages.
weights: logical indicating whether to include weights based on cell counts.
weightsByPair: logical indicating whether weights should be calculated for each cell type pair.
weightFactor: numeric that controls the convexity of the weight function.
window: Should the window around the regions be 'square', 'convex' or 'concave'.
window.length: A tuning parameter for controlling the level of concavity when estimating concave windows.
BPPARAM: A BiocParallelParam object.
sigma: A numeric variable used for scaling when fitting inhomogeneous L-curves.
Rs: A vector of radii that the measures of association should be calculated. If NULL, Rs = c(20, 50, 100) is specified by default.
minLambda: Minimum value for density for scaling when fitting inhomogeneous L-curves.
edgeCorrect: A logical indicating whether to perform edge correction.
includeZeroCells: A logical indicating whether to include cells with zero counts in the pairwise association calculation.
...: Other options.

Value

Data frame of p-values.

Examples

data("diabetesData")

# Test with random effect for patient on a pairwise combination of cell
# types.
spicy(diabetesData,
  condition = "stage", subject = "case",
  from = "Tc", to = "Th"
)
#> 
#> Number of cell type pairs: 1
#> Number of differentially localised cell type pairs: 
#> [1] 0

# Test all pairwise combinations of cell types without random effect of
# patient.
if (FALSE) { # \dontrun{
spicyTest <- spicy(diabetesData, condition = "stage", subject = "case")
} # }

# Test all pairwise combination of cell types with random effect of patient.
if (FALSE) { # \dontrun{
spicy(diabetesData, condition = "condition", subject = "subject")
} # }